I don't think there must be a reason. It could have been an unexpected result, ie a bug but a bug they decided not to fix or would have cost too much to fix.
No other mirrorless from other manufacturers do this. Obviously IS always on is not required as 2 of the 4 RF lenses that exist do not even have IS.
It's a PITA to have to turn off IS (or even think about it). There is a reason somewhere. If it was some sort of bug they would have fixed it before releasing the R.
Is this an obvious attempt to discourage the use of EF lens sooner than later since this isn't an issue with the new RF lenses with IS? Annoying, Canon.